[Bioc-devel] git svn dcommit

[Kasper Daniel Hansen]

So I have made some updates to minfi and they are "safe" in Github.  I now
want to commit them to Bioconductor.  I get pretty strange results,
although I never really understand what is going on.

1. I clone a fresh copy of minfi from Github.
2. I do
 # bash update_remotes.sh
(using proper path of course)
3. I do
 # git checkout devel
 # git svn rebase
 # git merge master --log
without any hiccups, and all seems to work so far.

Then I do
  # git svn dcommit --add-author-from

and hell starts (see output below).  What is kind of weird is that now it
wants me to do 241 (!!!!!) rebase.  And it starts to involve commits or
changes in files that haven't been touch for months.  This is really pretty
weird, given that I have completed the previous steps fine.

Any idea?  Otherwise I hope I can get special help at Stanford in a few
days ...

Best,
Kasper






$ git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/minfi ...
M DESCRIPTION

ERROR from SVN:
Item is out of date: Item '/trunk/madman/Rpacks/minfi/DESCRIPTION' is out
of date
W: 85e070dd7d7825132ca3e6399f2e4dc19195b627 and refs/remotes/git-svn-devel
differ, using rebase:
:100644 100644 0025283098af2a8f4376b1300533a4c5aabaea7b
8ac95ea78753b0a25d97c5debecbc6b2ead04ac0 M DESCRIPTION
:100644 100644 64a40f0b2655c7953ff154b42d6fa849e14462d3
92430c671d00d2131f5dc59cd3dbaa54679b585a M NAMESPACE
:040000 040000 732260942165586cd80d15ad9aa923e0969f604f
5098b8e0b0cabed337857680555df1ea6dc853f8 M R
:040000 040000 655f45f8ddd850a62a643151b73711c12ca0c5bb
9e9250da0089f89b9fb9ab986c617dbe66a3aab2 M inst
:040000 040000 3b781c09f0472bdff07ee734418b1bc263a31bd9
0f59f20b6cc89eaeeb94626a4445e3da26cef08f M man
:040000 040000 dd0723ff2712c28820000b81fafc1eb2de441e86
83da824cbedf66e528e93ba03abf4adb7e243669 M vignettes
First, rewinding head to replay your work on top of it...
Applying: updated citation information
Using index info to reconstruct a base tree...
.git/rebase-apply/patch:34: trailing whitespace.
 beanplot,
.git/rebase-apply/patch:35: trailing whitespace.
 RColorBrewer,
.git/rebase-apply/patch:36: trailing whitespace.
 nor1mix,
.git/rebase-apply/patch:37: trailing whitespace.
 siggenes,
.git/rebase-apply/patch:38: trailing whitespace.
 limma,
warning: squelched 287 whitespace errors
warning: 292 lines add whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging vignettes/minfi.bib
CONFLICT (add/add): Merge conflict in vignettes/minfi.bib
Auto-merging man/utils.Rd
CONFLICT (add/add): Merge conflict in man/utils.Rd
Auto-merging man/read.450k.sheet.Rd
CONFLICT (add/add): Merge conflict in man/read.450k.sheet.Rd
Auto-merging man/read.450k.exp.Rd
CONFLICT (add/add): Merge conflict in man/read.450k.exp.Rd
Auto-merging man/read.450k.Rd
CONFLICT (add/add): Merge conflict in man/read.450k.Rd
Auto-merging man/preprocessQuantile.Rd
CONFLICT (add/add): Merge conflict in man/preprocessQuantile.Rd
Auto-merging man/mdsPlot.Rd
CONFLICT (add/add): Merge conflict in man/mdsPlot.Rd
Auto-merging man/getAnnotation.Rd
CONFLICT (add/add): Merge conflict in man/getAnnotation.Rd
Auto-merging man/estimateCellCounts.Rd
CONFLICT (add/add): Merge conflict in man/estimateCellCounts.Rd
Auto-merging man/densityBeanPlot.Rd
CONFLICT (add/add): Merge conflict in man/densityBeanPlot.Rd
Auto-merging man/cpgCollapse.Rd
CONFLICT (add/add): Merge conflict in man/cpgCollapse.Rd
Auto-merging man/bumphunter.Rd
CONFLICT (add/add): Merge conflict in man/bumphunter.Rd
Auto-merging man/blockFinder.Rd
CONFLICT (add/add): Merge conflict in man/blockFinder.Rd
Auto-merging man/RGChannelSet-class.Rd
CONFLICT (add/add): Merge conflict in man/RGChannelSet-class.Rd
Auto-merging man/GenomicRatioSet-class.Rd
CONFLICT (add/add): Merge conflict in man/GenomicRatioSet-class.Rd
Auto-merging man/GenomicMethylSet-class.Rd
CONFLICT (add/add): Merge conflict in man/GenomicMethylSet-class.Rd
Auto-merging inst/unitTests/test_preprocess.R
CONFLICT (add/add): Merge conflict in inst/unitTests/test_preprocess.R
Auto-merging inst/NEWS.Rd
CONFLICT (add/add): Merge conflict in inst/NEWS.Rd
Auto-merging R/utils.R
CONFLICT (add/add): Merge conflict in R/utils.R
Auto-merging R/rset.R
CONFLICT (add/add): Merge conflict in R/rset.R
Auto-merging R/rgset.R
CONFLICT (add/add): Merge conflict in R/rgset.R
Auto-merging R/read.manifest.R
CONFLICT (add/add): Merge conflict in R/read.manifest.R
Auto-merging R/read.450k.R
CONFLICT (add/add): Merge conflict in R/read.450k.R
Auto-merging R/preprocessSwan.R
CONFLICT (add/add): Merge conflict in R/preprocessSwan.R
Auto-merging R/preprocess.R
CONFLICT (add/add): Merge conflict in R/preprocess.R
Auto-merging R/plot.R
CONFLICT (add/add): Merge conflict in R/plot.R
Auto-merging R/mset.R
CONFLICT (add/add): Merge conflict in R/mset.R
Auto-merging R/manifest.R
CONFLICT (add/add): Merge conflict in R/manifest.R
Auto-merging R/grset.R
CONFLICT (add/add): Merge conflict in R/grset.R
Auto-merging R/gmset.R
CONFLICT (add/add): Merge conflict in R/gmset.R
Auto-merging R/getSex.R
CONFLICT (add/add): Merge conflict in R/getSex.R
Auto-merging R/estimateCellCounts.R
CONFLICT (add/add): Merge conflict in R/estimateCellCounts.R
Auto-merging R/bumphunter.R
CONFLICT (add/add): Merge conflict in R/bumphunter.R
Auto-merging R/blocks.R
CONFLICT (add/add): Merge conflict in R/blocks.R
Auto-merging R/anno.R
CONFLICT (add/add): Merge conflict in R/anno.R
Auto-merging NAMESPACE
CONFLICT (add/add): Merge conflict in NAMESPACE
Auto-merging DESCRIPTION
CONFLICT (add/add): Merge conflict in DESCRIPTION
error: Failed to merge in the changes.
Patch failed at 0001 updated citation information
The copy of the patch that failed is found in: .git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase
--abort".

rebase refs/remotes/git-svn-devel: command returned error: 128

kaspers-air:~/Work/packages_github/minfi (devel *+|REBASE 1/241) $

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